Publications

@article{DBLP:journals/corr/abs-2012-09579,

title = {Towards Smart e-Infrastructures, A Community Driven Approach Based 

 on Real Datasets},

author = {Prashant Singh and Mona Mohamed Elamin and Salman Toor},

url = {https://arxiv.org/abs/2012.09579},

year  = {2020},

date = {2020-01-01},

journal = {CoRR},

volume = {abs/2012.09579},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-2003-11087,

title = {Bootstrapping Weakly Supervised Segmentation-free Word Spotting through 

 HMM-based Alignment},

author = {Tomas Wilkinson and Carl Nettelblad},

url = {https://arxiv.org/abs/2003.11087},

year  = {2020},

date = {2020-01-01},

journal = {CoRR},

volume = {abs/2003.11087},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/bioinformatics/WredeH19,

title = {Smart computational exploration of stochastic gene regulatory network 

 models using human-in-the-loop semi-supervised learning},

author = {Fredrik Wrede and Andreas Hellander},

url = {https://doi.org/10.1093/bioinformatics/btz420},

doi = {10.1093/BIOINFORMATICS/BTZ420},

year  = {2019},

date = {2019-01-01},

journal = {Bioinform.},

volume = {35},

number = {24},

pages = {5199–5206},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-1901-07335,

title = {Adapting The Secretary Hiring Problem for Optimal Hot-Cold Tier Placement 

 under Top-K Workloads},

author = {Ben Blamey and Fredrik Wrede and Johan Karlsson and Andreas Hellander and Salman Toor},

url = {http://arxiv.org/abs/1901.07335},

year  = {2019},

date = {2019-01-01},

journal = {CoRR},

volume = {abs/1901.07335},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-1912-09088,

title = {Resource- and Message Size-Aware Scheduling of Stream Processing at 

 the Edge with application to Realtime Microscopy},

author = {Ben Blamey and Ida-Maria Sintorn and Andreas Hellander and Salman Toor},

url = {http://arxiv.org/abs/1912.09088},

year  = {2019},

date = {2019-01-01},

journal = {CoRR},

volume = {abs/1912.09088},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/peerj-cs/CapucciniLCNSGT19,

title = {On-demand virtual research environments using microservices},

author = {Marco Capuccini and Anders Larsson and Matteo Carone and Jon Ander Novella and Noureddin Sadawi and Jianliang Gao and Salman Toor and Ola Spjuth},

url = {https://doi.org/10.7717/peerj-cs.232},

doi = {10.7717/PEERJ-CS.232},

year  = {2019},

date = {2019-01-01},

journal = {PeerJ Comput. Sci.},

volume = {5},

pages = {e232},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-1910-14029,

title = {Flash X-ray diffraction imaging in 3D: a proposed analysis pipeline},

author = {Jing Liu and Stefan Engblom and Carl Nettelblad},

url = {http://arxiv.org/abs/1910.14029},

year  = {2019},

date = {2019-01-01},

journal = {CoRR},

volume = {abs/1910.14029},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{singh2018multi,

title = {Multi-statistic approximate Bayesian computation with multi-armed bandits},

author = {Prashant Singh and Andreas Hellander},

year  = {2018},

date = {2018-01-01},

journal = {arXiv preprint arXiv:1805.08647},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/bmcbi/AusmeesJTHN18,

title = {BAMSI: a multi-cloud service for scalable distributed filtering 

 of massive genome data},

author = {Kristiina Ausmees and Aji John and Salman Zubair Toor and Andreas Hellander and Carl Nettelblad},

url = {https://doi.org/10.1186/s12859-018-2241-z},

doi = {10.1186/S12859-018-2241-Z},

year  = {2018},

date = {2018-01-01},

journal = {BMC Bioinform.},

volume = {19},

number = {1},

pages = {240:1–240:11},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-1805-08647,

title = {Multi-Statistic Approximate Bayesian Computation with Multi-Armed 

 Bandits},

author = {Prashant Singh and Andreas Hellander},

url = {http://arxiv.org/abs/1805.08647},

year  = {2018},

date = {2018-01-01},

journal = {CoRR},

volume = {abs/1805.08647},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-1807-07724,

title = {Apache Spark Streaming and HarmonicIO: A Performance and Architecture 

 Comparison},

author = {Ben Blamey and Andreas Hellander and Salman Zubair Toor},

url = {http://arxiv.org/abs/1807.07724},

year  = {2018},

date = {2018-01-01},

journal = {CoRR},

volume = {abs/1807.07724},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/jcheminf/AhmedGCTSLS18,

title = {Efficient iterative virtual screening with Apache Spark and conformal 

 prediction},

author = {Laeeq Ahmed and Valentin Georgiev and Marco Capuccini and Salman Zubair Toor and Wesley Schaal and Erwin Laure and Ola Spjuth},

url = {https://doi.org/10.1186/s13321-018-0265-z},

doi = {10.1186/S13321-018-0265-Z},

year  = {2018},

date = {2018-01-01},

journal = {J. Cheminformatics},

volume = {10},

number = {1},

pages = {8:1–8:8},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/tsc/OsmaniTKKLWKET18,

title = {Secure Cloud Connectivity for Scientific Applications},

author = {Lirim Osmani and Salman Toor and Miika Komu and Matti J. Kortelainen and Tomas Lindén and John White and Rasib Hassan Khan and Paula Eerola and Sasu Tarkoma},

url = {https://doi.org/10.1109/TSC.2015.2469292},

doi = {10.1109/TSC.2015.2469292},

year  = {2018},

date = {2018-01-01},

journal = {IEEE Trans. Serv. Comput.},

volume = {11},

number = {4},

pages = {658–670},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-1805-06180,

title = {KubeNow: an On-Demand Cloud-Agnostic Platform for Microservices-Based 

 Research Environments},

author = {Marco Capuccini and Anders Larsson and Matteo Carone and Jon Ander Novella and Noureddin Sadawi and Jianliang Gao and Salman Zubair Toor and Ola Spjuth},

url = {http://arxiv.org/abs/1805.06180},

year  = {2018},

date = {2018-01-01},

journal = {CoRR},

volume = {abs/1805.06180},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-1808-02318,

title = {MaRe: Container-Based Parallel Computing with Data Locality},

author = {Marco Capuccini and Salman Zubair Toor and Staffan Arvidsson and Ola Spjuth},

url = {http://arxiv.org/abs/1808.02318},

year  = {2018},

date = {2018-01-01},

journal = {CoRR},

volume = {abs/1808.02318},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-1804-06724,

title = {Using Convex Optimization of Autocorrelation with Constrained Support 

 and Windowing for Improved Phase Retrieval Accuracy},

author = {Alberto Pietrini and Carl Nettelblad},

url = {http://arxiv.org/abs/1804.06724},

year  = {2018},

date = {2018-01-01},

journal = {CoRR},

volume = {abs/1804.06724},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{singh2017sequential,

title = {A sequential sampling strategy for adaptive classification of computationally expensive data},

author = {Prashant Singh and Joachim van der Herten and Dirk Deschrijver and Ivo Couckuyt and Tom Dhaene},

year  = {2017},

date = {2017-01-01},

journal = {Structural and Multidisciplinary Optimization},

volume = {55},

pages = {1425–1438},

publisher = {Springer Berlin Heidelberg},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{singh2017constrained,

title = {Constrained multi-objective antenna design optimization using surrogates},

author = {Prashant Singh and Marco Rossi and Ivo Couckuyt and Dirk Deschrijver and Hendrik Rogier and Tom Dhaene},

year  = {2017},

date = {2017-01-01},

journal = {International Journal of Numerical Modelling: Electronic Networks, Devices and Fields},

volume = {30},

number = {6},

pages = {e2248},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{singh2017multi,

title = {Multi-objective geometry optimization of a gas cyclone using triple-fidelity co-kriging surrogate models},

author = {Prashant Singh and Ivo Couckuyt and Khairy Elsayed and Dirk Deschrijver and Tom Dhaene},

year  = {2017},

date = {2017-01-01},

journal = {Journal of Optimization Theory and Applications},

volume = {175},

pages = {172–193},

publisher = {Springer US},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/siamam/HellanderKLM17,

title = {Robustness Analysis of Spatiotemporal Models in the Presence of Extrinsic 

 Fluctuations},

author = {Andreas Hellander and Jan Klosa and Per Lötstedt and Shev MacNamara},

url = {https://doi.org/10.1137/15M1052317},

doi = {10.1137/15M1052317},

year  = {2017},

date = {2017-01-01},

journal = {SIAM J. Appl. Math.},

volume = {77},

number = {4},

pages = {1157–1183},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/tcbb/MahjaniTNH17,

title = {A Flexible Computational Framework Using R and Map-Reduce for Permutation 

 Tests of Massive Genetic Analysis of Complex Traits},

author = {Behrang Mahjani and Salman Zubair Toor and Carl Nettelblad and Sverker Holmgren},

url = {https://doi.org/10.1109/TCBB.2016.2527639},

doi = {10.1109/TCBB.2016.2527639},

year  = {2017},

date = {2017-01-01},

journal = {IEEE ACM Trans. Comput. Biol. Bioinform.},

volume = {14},

number = {2},

pages = {381–392},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/EngblomNL17,

title = {Assessing Uncertainties in X-ray Single-particle Three-dimensional 

 reconstructions},

author = {Stefan Engblom and Carl Nettelblad and Jing Liu},

url = {http://arxiv.org/abs/1701.00338},

year  = {2017},

date = {2017-01-01},

journal = {CoRR},

volume = {abs/1701.00338},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{singh2016shape,

title = {Shape optimization of a cyclone separator using multi-objective surrogate-based optimization},

author = {Prashant Singh and Ivo Couckuyt and Khairy Elsayed and Dirk Deschrijver and Tom Dhaene},

year  = {2016},

date = {2016-01-01},

journal = {Applied Mathematical Modelling},

volume = {40},

number = {5-6},

pages = {4248–4259},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{singh2016automated,

title = {Automated line-based sequential sampling and modeling algorithm for EMC near-field scanning},

author = {Prashant Singh and Tim Claeys and Guy AE Vandenbosch and Davy Pissoort},

year  = {2016},

date = {2016-01-01},

journal = {IEEE Transactions on Electromagnetic Compatibility},

volume = {59},

number = {2},

pages = {704–709},

publisher = {IEEE},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{gong2016measurement,

title = {Measurement-based wireless network planning, monitoring, and reconfiguration solution for robust radio communications in indoor factories},

author = {Xu Gong and Jens Trogh and Quentin Braet and Emmeric Tanghe and Prashant Singh and David Plets and Jeroen Hoebeke and Dirk Deschrijver and Tom Dhaene and Luc Martens and others},

year  = {2016},

date = {2016-01-01},

journal = {IET Science, Measurement & Technology},

volume = {10},

number = {4},

pages = {375–382},

publisher = {The Institution of Engineering and Technology},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/mmas/BlancEHL16,

title = {Mesoscopic Modeling of Stochastic Reaction-Diffusion Kinetics in the 

 Subdiffusive Regime},

author = {Emilie Blanc and Stefan Engblom and Andreas Hellander and Per Lötstedt},

url = {https://doi.org/10.1137/15M1013110},

doi = {10.1137/15M1013110},

year  = {2016},

date = {2016-01-01},

journal = {Multiscale Model. Simul.},

volume = {14},

number = {2},

pages = {668–707},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/ploscb/DrawertHBBBDDGG16,

title = {Stochastic Simulation Service: Bridging the Gap between the Computational 

 Expert and the Biologist},

author = {Brian Drawert and Andreas Hellander and Benjamin B. Bales and Debjani Banerjee and Giovanni Bellesia and Bernie J. Daigle Jr. and Geoffrey Douglas and Mengyuan Gu and Anand Gupta and Stefan Hellander and Christopher B. Horuk and Dibyendu Nath and Aviral Takkar and Sheng Wu and Per Lötstedt and Chandra Krintz and Linda R. Petzold},

url = {https://doi.org/10.1371/journal.pcbi.1005220},

doi = {10.1371/JOURNAL.PCBI.1005220},

year  = {2016},

date = {2016-01-01},

journal = {PLoS Comput. Biol.},

volume = {12},

number = {12},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/siamsc/MeineckeEHL16,

title = {Analysis and Design of Jump Coefficients in Discrete Stochastic Diffusion 

 Models},

author = {Lina Meinecke and Stefan Engblom and Andreas Hellander and Per Lötstedt},

url = {https://doi.org/10.1137/15M101110X},

doi = {10.1137/15M101110X},

year  = {2016},

date = {2016-01-01},

journal = {SIAM J. Sci. Comput.},

volume = {38},

number = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/siamsc/DrawertTTPH16,

title = {MOLNs: A Cloud Platform for Interactive, Reproducible, and Scalable 

 Spatial Stochastic Computational Experiments in Systems Biology Using 

 PyURDME},

author = {Brian Drawert and Michael Trogdon and Salman Zubair Toor and Linda R. Petzold and Andreas Hellander},

url = {https://doi.org/10.1137/15M1014784},

doi = {10.1137/15M1014784},

year  = {2016},

date = {2016-01-01},

journal = {SIAM J. Sci. Comput.},

volume = {38},

number = {3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/NettelbladN16,

title = {CannyFS: Opportunistically Maximizing I/O Throughput Exploiting 

 the Transactional Nature of Batch-Mode Data Processing},

author = {Jessica Nettelblad and Carl Nettelblad},

url = {http://arxiv.org/abs/1612.06830},

year  = {2016},

date = {2016-01-01},

journal = {CoRR},

volume = {abs/1612.06830},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/DrawertTTPH15,

title = {MOLNs: A cloud platform for interactive, reproducible and scalable 

 spatial stochastic computational experiments in systems biology using 

 PyURDME},

author = {Brian Drawert and Michael Trogdon and Salman Zubair Toor and Linda R. Petzold and Andreas Hellander},

url = {http://arxiv.org/abs/1508.03604},

year  = {2015},

date = {2015-01-01},

journal = {CoRR},

volume = {abs/1508.03604},

keywords = {},

pubstate = {published},

tppubtype = {article}

}